Rapid advances in genome sequencing techniques and throughput are providing scientists with increasingly detailed views of individual genomes, furthering our understanding of genetic variation in a wide array of organisms, of human population history and of the biology of Mendelian disorders and complex traits. Experiments that were until recently restricted to very large genome centers, such as the resequencing of human genomes, can now be carried out by a wide range of investigators. While these technological advances will enable many new discoveries in human and model organism genetics, they also pose formidable computational challenges. RFA-HG-10-018, entitled Informatics Tools for High-Throughput Sequence Data Analysis, is intended to fund further development of existing software to ensure that any biological or biomedical research laboratory can benefit from advances in sequencing technologies. We have developed specialized, state-of-the-art tools for the processing and analysis of next generation sequence data. Our tools encompass many key steps in sequence data analysis, ranging from quality control, to read mapping, to the identification, genotyping and annotation of many classes of sequence variation, to downstream association analyses that seek to connect identified variants with organismal phenotypes. These tools have been used to support analysis of several large, challenging datasets including not only data from the 1000 Genomes Project but also >1000 whole genomes and >2500 exomes sequenced in medical sequencing projects. Here, we propose to develop these tools into easy-to-use, portable, well-documented packages and complete pipelines that facilitate biomedical research in a wide variety of settings. A key component of the proposal is the deployment of these tools in the Galaxy cloud, where they will be accessible to investigators without direct access to a local high-throughput computing and data storage facility.